GIRI (Grinding, Imaging and Reconstruction Instrument), the centerpiece of the newly constructed Princeton Grinder Lab, is a fully automated rock grinder equipped with a high-resolution camera. GIRI's photos are used to create 3-D models that let scientists examine the inner features of rocks, which can include tiny fossils of ancient life forms. Above is a rock sample containing 650 million-year-old fossilized sponges as they appear to the naked eye (top) and when photographed by GIRI. (Courtesy of Adam Maloof, the Princeton Grinder Lab and Situ Studio)

Posted August 15, 2013; 12:00 p.m.

by Morgan Kelly, Office of Communications

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GIRI grinds away 1 micron of rock layer at a time, then snaps a photo of each new layer with an 80-megapixel camera. The photos are then segmented and digitally reconstructed into a 3-D model. This video shows the grinding, imaging and 3-D modeling process for an oolite sample that is approximately 450 million years old. The sample contains nearly spherical grains of calcium carbonate sediment known as ooids. Because of their large and consistent porosity, these oolites are important petroleum reservoir rocks, especially in regions like the Middle East. (Courtesy of the Princeton Grinder Lab and Situ Studio)

Possibly more intriguing than Adam Maloof inadvertently uncovering the oldest known animal fossils was what he had to do to examine them.

The remains of what would turn out to be circa 650 million-year-old sponge-like animals appeared as little more than red streaks embedded in a chunk of limestone Maloof collected in Australia while originally searching for evidence of "snowball Earth," the hypothesized deep-freeze the entire planet succumbed to about 650 million years ago.

To study these crimson oddities, Maloof, a Princeton University associate professor of geosciences, and former graduate student Catherine Rose ground away by hand 50 microns — roughly half the width of a human hair — of rock a layer at a time, taking a photo of each new layer. The plan was to digitally stack each photo to produce a 3-D model that would allow a full view of the fossils' structure, and a more certain identification.

The work dragged. After the equivalent of toiling all day, every day for two weeks, the researchers had sheared off only a disheartening 2 centimeters of limestone. The photo quality fluctuated between light and dark, and the shots did not line up properly. Maloof and his group tried drilling lead holes into the rock so that images could be registered to a fixed position, but "drilling straight holes at 50-micron tolerances is very difficult," Maloof said.

But it all paid off: In 2010, Maloof and Rose were first and second author, respectively, of a paper in the journal Nature Geosciences reporting that the sponge-like organisms were roughly 70 million years older than any animal fossil yet discovered.

GIRI generates a 3-D fossil model similar to how stop-motion animation is created. When photos of each rock layer are viewed consecutively, features in the rock appear to move. In the video above, details of an oolite sample change shape as GIRI grinds away a total of 25 microns, or one-fourth the width of a human hair. (Courtesy of the Princeton Grinder Lab)

It also was the springboard for Maloof to establish the newly constructed Princeton Grinder Lab located in a specially designed building that opened behind Guyot Hall in February, and is funded by the National Science Foundation and the University. The lab's centerpiece is the solution to every hardship Maloof faced working that one piece of limestone — an automated, high-precision industrial grinder equipped with a high-resolution camera. The machine can grind and image a rock sample in as little as one hour, or as long as a few days, depending on the desired resolution. And the sample never leaves the machine, allowing for consistently angled and lit photos.

Adam Maloof (above), a Princeton associate professor of geosciences, co-developed GIRI with Brooklyn-based Situ Studio after one of Maloof's graduate students spent the equivalent of 14 days straight in 2010 grinding and photographing a rock sample by hand to shear off only a disheartening 2 centimeters. That sample contained 650 million-year-old sponge-like organisms that turned out to be the oldest animal fossils yet discovered. GIRI can grind and image a rock sample in as little as one hour, or as long as a few days, depending on the desired resolution. (Courtesy of the Princeton Grinder Lab and Christine Chen)

This is GIRI. Unique for its automation and precision, the Grinding, Imaging and Reconstruction Instrument was designed in collaboration with Brooklyn-based Situ Studio, which helped generate the 3-D models for the 2010 Nature Geoscience paper.

The machine is an 8,000-pound goliath with a gentle touch. Intended for machining metal, GIRI is equipped with a diamond-coated grinding wheel that clocks 3,000 rpms yet can nimbly remove layers of rock as small as 1 micron. Its agility is why GIRI sits atop an isolated concrete pad in a room built with sand-insulated blocks — at these scales the slightest vibration or temperature change can displace the grinder stone by hundreds of microns.

Like a car wash, GIRI rinses the sample free of dust as it's ground, gives it a once-over with a squeegee developed with lab scientist Alex Spatzier, then positions the sample beneath an auto-retracting camera housing. An 80-megapixel camera with a 4x5.4 cm sensor (the average consumer camera is 12-16 megapixels on a 3.6x2.4 cm sensor) takes a shot. Then the sample goes through the whole cycle again.

The images are wired to computers in an adjacent control room separated from GIRI by a window and an airlock. Anyone familiar with Claymation and stop-motion animation may be able to grasp how GIRI generates a 3-D fossil model. As each layer is ground away, different features within the rock are revealed. When the photos are viewed consecutively, features in the rock gyrate, shrink, expand, disappear and emerge in a rush of activity one rarely equates with rocks. When formed into one digital block, the photos provide a 360-degree view of the rock's internal characteristics, and those details can be extracted and further analyzed.

GIRI is an extremely high-tech variation of an old method known as serial sectioning, which, in its simplest form, entails removing a layer of rock and hand-drawing the details. GIRI is equipped with a diamond-coated grinding wheel (above) that moves at 3,000 rpms, yet can remove layers of rock as small as 1 micron. At these scales, the slightest vibration or temperature change can displace the grinder stone by hundreds of microns, so GIRI sits atop an isolated concrete pad in a room built with sand-insulated blocks. (Courtesy of the Princeton Grinder Lab and Situ Studio)

In the classroom, GIRI can enhance students' field and research experience, Maloof said. Many of the courses he teaches include fieldwork, such as "Sedimentology," which includes trips to the New Jersey Pine Barrens, the Bahamas, Kentucky and the Catskills. A geophysical survey in Cyprus accompanies the course "Earth's Environments and Ancient Civilizations" that Maloof teaches with Associate Professor of Geosciences Frederik Simons.

"Students usually collect samples and analyze them under the microscope or on the mass spectrometer," Maloof said, "but now they will be able to image 3-D structures within those rock samples — everything from air bubbles in basalt and fossils in limestone, to the delicate compositions of ceramics that indicate when and where the vessel likely was made."

GIRI is an extremely high-tech variation of an old method known as serial sectioning, Maloof said. In its most basic form, serial sectioning entails removing a layer of rock and hand-drawing the details. "People continue and have continued to do this — we're just the first to automate it," Maloof said. "People can produce high-quality images and more accurate 3-D models in a much shorter timeframe using GIRI. There's nothing like this in the world."

The traditional tedium of serial sectioning has put the method at a disadvantage when compared with modern imaging technology such as X-ray scanning and computerized tomography, or CT. While quicker and still effective, and a boon to the health sciences, those methods have difficulty in the crossover from flesh to rock, Maloof and Spatzier explained. GIRI was intended to combine the speed of imaging technology with the sharp frame-by-frame detail inherent in serial sectioning.

A good X-ray can capture 1-micron details, but only near a rock's surface — the radiation peters out the deeper it goes into the rock and the image becomes obscured, Spatzier said. Non-invasive imaging technology also relies on the various densities within the object being scanned, Maloof said. In a human, blood, bone and flesh have different densities that make for clear images. In a rock, such as the one studied for the 2010 paper, the fossils often have the same density as the limestone matrix surrounding it, Maloof said.

"If we had scanned that it would have looked like a big blob," Maloof said. "Many of the fossils in the world are shell and limestone with no density contrast. With GIRI, we can see micron-scale features in color and texture consistently over tens of centimeters of rock. With every image we can see the objects in every slice, and check the model reconstructions with the naked eye. The only disadvantage is that GIRI grinds the sample to dust."

But important discoveries can be hidden away in those samples, and serial sectioning GIRI-style might be the best way to access them, Maloof said.

"We kept seeing these weird red shapes, and couldn't determine what they were," he said about his storied limestone sample. "Some looked like fossils, some didn't. We just ignored them for years because we had no way to analyze them."

Stromatolites as old as this 635 million-year-old sample photographed by GIRI typically built up as sediment was trapped and bound by layers of bacteria. Frequently, stromatolites were formed by cyanobacteria, or blue-green algae, photosynthesizing in shallow water under a thin film of mud that protected them from ultraviolet radiation. The 3-D morphology of these rocks records important information about the environment they formed in, such as current and wave energy, and water chemistry. Many scientists think that older stromatolites are the most ancient evidence of life on Earth. (Courtesy of the Princeton Grinder Lab)

Those sponge fossils fell instantly into a debate about when Earth first hosted animals. Some scientists had indirect molecular-clock and geochemical evidence that suggested animals predated snowball Earth. Others believed that the lack of body-fossil evidence made it more likely that animals evolved after the most recent snowball Earth episode. Maloof and his co-authors showed that sponges had set up in bacterial reefs before the glaciation, and essentially extended the known presence of animals on Earth by millions of years.

"Prior to our work, only two groups proposed that sponges should exist at this time," Maloof said. "Two groups of independent scientists said that these animals should exist despite no record. Fossil experts were saying that's unlikely. Since our paper, two other papers have found 'textures' left by sponge-like creatures in even older rocks, and other groups are starting to describe possible body fossils."

With GIRI operational — after months of programming and tinkering with cycle timing, Spatzier said — the Grinder Lab has begun accepting samples to be analyzed, and researchers from other institutions are already slated to use GIRI themselves. Maloof hopes that the lab, buttressed by GIRI's capabilities, can become a destination facility for other scientists.

"My long-term plan is to let researchers from other institutions come here for a week and run their own samples," Maloof said. "Ideally, GIRI will host a bustling lab filled with scientists eager to turn enigmatic two-dimensional shapes seen on the surfaces of rocks into quantitative three-dimensional models of objects that will inspire their research."

This 650 million-year-old oolite photographed by GIRI contains ooids nearly 1 centimeter in diameter, and are indicative of the "giant oolite problem." Ooids form when the nuclei of calcium carbonate on the sea floor produce new layers as they are continuously agitated by waves. In the modern ocean, ooids form spheres only 1-2 millimeters in size. While this sample contains millimeter-scale ooids, the giant ooids are so large that scientists wonder if the ancient ocean had to be more viscous and energetic in order to frequently move these large grains around and allow for the formation of nearly concentric, spherical layers. Understanding the 3-D structure of these giant ooids and comparing them to the smaller ooids that must have formed at the same time will help solve this paradox. (Courtesy of the Princeton Grinder Lab)